A small group protest out the front of the Darwin Supreme Court where hearings are underway.

ABC News: Avani Dias

The Northern Territory Department of Children and Families was "impenetrable" and "secretive", a former NT ombudsman has told the Royal Commission into the Protection and Detention of Children.

Carolyn Richards also told the inquiry she had powers to investigate the child protection system taken away from her by a former Labor minister.

The royal commission was prompted by the ABC's Four Corners program, which detailed years of abuse in the Don Dale youth detention centre in the Northern Territory.

As well as the issue of detention, the child protection system more broadly is being examined.

Ms Richards told the commission that she wrote a report on child protection issues prompted by concerns from health workers about a lack of communication with the Department of Children and Families.

She said poor communication from the department's Central Intake Service meant health workers were unable to assess whether it was safe to release children from hospital.

The Central Intake Service was the unit in the department that assessed children and decided what priority they should receive, but Ms Richards said they often did not answer their phones, which caused serious problems for health workers.

"When they were dealing with a child that was in hospital and trying to do discharge planning or work out if it was safe to send a child home, they were acting without any real knowledge, if anything, about what the department was going to do," she said.

Midway through writing that report then minister Kon Vatskalis phoned her to say he was taking away her power to investigate the child protection system.

"I was informed by the minister for child protection that legislation was about to be passed to remove my powers to investigate matters relating to child protection," she said.

But Ms Richards pushed on with her investigation anyway.

"There were children actually being neglected and abused, they were being badly managed ... and I thought it needed to be looked at," she said.

Children's commissioner paints grim picture

Earlier on Tuesday, the national children's commissioner, Megan Mitchell, painted a grim picture of Darwin's Don Dale Youth Detention Centre, telling the inquiry that children were frequently and routinely isolated for very long periods in the hot, ageing facility.

"I just have to say that the facility itself is old and ageing and things are broken and toilets are rusty and as I said before there is no air conditioning," the children's commissioner told the hearing.

"It is very hot, there is minimal air flow and there are these extensive periods of isolation and use of force and I think all of those things are breaches of children's rights."

She said isolation was used routinely and frequently.

"When I say frequently and routinely, you know, 23 hours a day for several weeks that some young people in the high-security, the maximum-security area, was an absolute concern," she said.

"When I asked the young people about how they felt in that environment, some of the words they said were depressed, angry, sad and like a caged animal."

The royal commission was prompted by the ABC's Four Corners program, which detailed years of abuse in youth detention centres in the Northern Territory.

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Children at the facility did not usually make complaints about the situation because many were concerned about retribution from staff, she said, or thought they may be considered "a snitch".

Counsel assisting the commission, Peter Callaghan SC, said there had been more than 50 reports into issues being investigated that were relevant to the royal commission already.

"Do we need to confront some sort of inquiry mentality in which investigation is allowed as a substitution for action and reporting is accepted as a replacement for results?" Mr Callaghan said in his opening address.

NT Government will not pay for former A-G to be represented

The royal commission also heard from Andrew Harris, SC, who had been retained to represent the NT's former attorney-general John Elferink.

Mr Harris said the new government in the NT, elected in August, had withdrawn its offer to pay for Mr Elferink's ongoing legal representation.

"Our instructions to appear for Mr Elferink from the NT Government, at the cost of the NT Government, have been terminated," he said.

He added Mr Elferink did not have the "financial wherewithal" to fund the representation himself.

But the NT Attorney General Natasha Fyles said Mr Elferink had already received $57,000 in funding.

"$57,000 is a significant amount of legal representation that has been paid for Mr Elferink, considering today is the first day of hearings and Mr Elferink has not yet been called as a witness," she said.

Ms Fyles said Mr Elferink could apply for more money throughout the royal commission.

"But we need to make sure we protect the tax payer dollar so it's not an open blank cheque book for lawyers," she said.